Researchers have discovered that, in the influenza virus, being the most beneficial mutation is no guarantee of
long-term genetic success.

Wellcome Trust Sanger Institute scientists have used computer modelling to understand why some mutations in a virus
gene rise to dominance and become 'fixed' in the genome of the virus, while others die out. Their findings were based
upon real-world observations of the evolution of a human flu virus, using genome sequences collected over many years by
researchers worldwide.

The team studied mutations in the haemagglutinin gene of the human influenza virus A/H3N2, which latches the virus on
to human cells during an infection. Using a computer model, the team identified three key factors that determine the
long-term survival of a mutation. The three factors are: the benefit the mutation confers to the virus; the background
of other mutations that were present in the gene when the mutation appeared; and the effect of subsequent competition
from different versions of the same gene in sibling viruses. To test the influence of each of these factors, they
applied their model to the changes seen in the haemagglutinin gene between 1996 and the present day.

"We are keen to understand how evolutionary selection within the flu virus works over time and
around the world," says Dr Chris Illingworth, first author of the study, from the Sanger Institute. "In some ways, the flu virus is very simple. When a person catches flu, their cells become incubators for the
virus. Within each cell, the virus produces copies of itself. However, the evolution of the virus is not so simple. The
copying process is highly error-prone, so that the new viruses often contain mutations. New mutations can either help
or hinder the virus from spreading. But having the best mutation doesn't guarantee evolutionary success.

"Previous approaches to studying viral evolution have often thought about mutations one at a time, in isolation from
each other. But at any one time, a large number of mutations exist. Viruses with different sets of mutations compete
against each other, and the combined effect of all of the mutations must be taken into account."

" For the first time, we are able to study the adaptive dynamics of a viral population at the level of individual
mutations. "

Chris Illingworth

The computer model developed by the researchers considered the benefit, or disadvantage, of each mutation, but also
looked at whether pairs of mutations appeared together (in the same virus), or apart (in different viruses). In the
model, beneficial mutations in the same virus help each other out, while beneficial mutations in different viruses
compete. In the haemagglutinin gene of human influenza A/H3N2 an average of seven new mutations fix in the virus
population each year. By analysing which gene variations became dominant and which did not since 1996, the team arrived
at their result.

"You might expect that the most beneficial single mutation in a gene would always be the most
successful in fixing into the virus' genome, but this is not what we found," explains Dr Ville Mustonen, senior
author of the paper, from the Sanger Institute. "Our analysis of genome sequences of the influenza
virus reveals that two other factors are important for a mutation's success: the sequence of the version of the gene
upon which a mutation appeared (how beneficial or not other mutations within the gene are) and the competition from
other forms of the gene with different mutations."

The computer model developed by the team built on methods they had employed for studying evolution in a population
using genetic sequence data collected across multiple points in time. The approach accounted for the fact that positive
selection - where a beneficial mutation enables a virus to thrive - affects the other mutations occurring across the
virus gene, either for their benefit, or for their loss. For example, an unhelpful mutation could succeed if it was
coupled to a very beneficial mutation further along the gene - hitchhiking to success. However, a weakly beneficial
mutation, if it was opposed by another, stronger mutation, could be caused to die out.

"For the first time, we are able to study the adaptive dynamics of a viral population at the level
of individual mutations," adds Chris Illingworth. "We can do this because our method looks
at selection across the entire gene, estimating both the relative benefit of the genomic background upon which the
mutation appeared, and the combined effect of interference from other mutations on the genome over its lifetime.
Statistically, we found that mutations were more likely to become fixed in the flu population if they were beneficial
for the virus, had been fortunate to appear on more beneficial backgrounds, and had encountered less opposition from
other mutations."

The new computer model could potentially aid in predicting how the flu virus might change in the future. However,
further research is needed to discover the true potential of this approach. "We need to be cautious
before making bold claims," says Ville Mustonen. "Our mathematical model, like all such
approaches, is based on a number of assumptions. The next question to answer is whether or not the model matches
reality closely enough to make useful predictions."

Notes to Editors

Publication details

Components of selection in the evolution of the influenza virus: linkage effects beat inherent selection.

The Wellcome Trust Sanger Institute

The Wellcome Trust Sanger Institute is one of the world's leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease.

Website

The Wellcome Trust

The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests.